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// $Id$
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/**
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* Copyright (C) 2014 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.taxeditor.molecular.editor;
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import info.bioinfweb.commons.swt.SWTUtils;
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import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
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import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;
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import info.bioinfweb.libralign.alignmentarea.tokenpainter.NucleotideTokenPainter;
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import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
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import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;
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import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
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import info.bioinfweb.libralign.editsettings.EditSettingsChangeEvent;
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import info.bioinfweb.libralign.editsettings.EditSettingsListener;
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import info.bioinfweb.libralign.model.AlignmentModel;
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import info.bioinfweb.libralign.model.AlignmentModelChangeListener;
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import info.bioinfweb.libralign.model.AlignmentModelUtils;
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import info.bioinfweb.libralign.model.adapters.StringAdapter;
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import info.bioinfweb.libralign.model.events.SequenceChangeEvent;
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import info.bioinfweb.libralign.model.events.SequenceRenamedEvent;
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import info.bioinfweb.libralign.model.events.TokenChangeEvent;
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import info.bioinfweb.libralign.model.implementations.PackedAlignmentModel;
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import info.bioinfweb.libralign.model.tokenset.CharacterTokenSet;
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import info.bioinfweb.libralign.model.tokenset.TokenSet;
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import info.bioinfweb.libralign.multiplealignments.AlignmentAreaList;
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import info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer;
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import info.bioinfweb.libralign.pherogram.model.PherogramAreaModel;
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import info.bioinfweb.libralign.pherogram.model.ShiftChange;
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import info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider;
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import info.bioinfweb.libralign.pherogram.provider.PherogramProvider;
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import info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider;
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import info.bioinfweb.tic.SWTComponentFactory;
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import java.io.File;
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import java.io.IOException;
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import java.io.InputStream;
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import java.net.URI;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.TreeMap;
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import org.biojava.bio.chromatogram.ChromatogramFactory;
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import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
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import org.eclipse.core.runtime.IProgressMonitor;
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import org.eclipse.swt.SWT;
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import org.eclipse.swt.dnd.Clipboard;
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import org.eclipse.swt.widgets.Composite;
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import org.eclipse.swt.widgets.Display;
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import org.eclipse.ui.IActionBars;
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import org.eclipse.ui.IEditorInput;
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import org.eclipse.ui.IEditorPart;
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import org.eclipse.ui.IEditorSite;
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import org.eclipse.ui.PartInitException;
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import org.eclipse.ui.PlatformUI;
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import org.eclipse.ui.commands.ICommandService;
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import org.eclipse.ui.part.EditorPart;
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import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
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import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
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import eu.etaxonomy.cdm.model.media.MediaUtils;
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import eu.etaxonomy.cdm.model.molecular.Sequence;
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import eu.etaxonomy.cdm.model.molecular.SequenceString;
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import eu.etaxonomy.cdm.model.molecular.SingleRead;
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import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
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import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment.Shift;
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import eu.etaxonomy.taxeditor.model.MessagingUtils;
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import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
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import eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler;
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import eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler;
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import eu.etaxonomy.taxeditor.store.CdmStore;
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import eu.etaxonomy.taxeditor.view.derivateSearch.DerivateLabelProvider;
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/**
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* Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to
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* a consensus sequence.
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* <p>
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* The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>.
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*
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* @author Ben Stöver
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* @author pplitzner
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* @date 04.08.2014
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*/
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public class AlignmentEditor extends EditorPart {
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public static final String ID = "eu.etaxonomy.taxeditor.molecular.AlignmentEditor";
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public static final int READS_AREA_INDEX = 1;
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public static final int EDITABLE_CONSENSUS_AREA_INDEX = READS_AREA_INDEX + 1;
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public static final int CONSENSUS_HINT_AREA_INDEX = EDITABLE_CONSENSUS_AREA_INDEX + 1;
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public static final int PHEROGRAM_AREA_INDEX = 0;
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public static final int CONSENSUS_DATA_AREA_INDEX = 0;
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public static final String DEFAULT_READ_NAME_PREFIX = "Read ";
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public static final String CONSENSUS_NAME = "Consensus";
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private final ConversationHolder conversationHolder;
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private final AlignmentModelChangeListener DIRTY_LISTENER = new AlignmentModelChangeListener() {
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@Override
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public <T> void afterTokenChange(TokenChangeEvent<T> e) {
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setDirty();
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}
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@Override
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public <T> void afterSequenceRenamed(SequenceRenamedEvent<T> e) {
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setDirty();
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}
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@Override
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public <T> void afterSequenceChange(SequenceChangeEvent<T> e) {
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setDirty();
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}
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@Override
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public <T, U> void afterProviderChanged(AlignmentModel<T> oldProvider,
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AlignmentModel<U> newProvider) { // Not expected.
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setDirty();
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}
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};
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private final AlignmentEditorActionUpdater ACTION_UPDATER = new AlignmentEditorActionUpdater();
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public final Clipboard CLIPBOARD = new Clipboard(Display.getCurrent()); //TODO Move to global EDITor class.
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private MultipleAlignmentsContainer alignmentsContainer = null;
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private final Map<Integer, SingleReadAlignment> cdmMap = new TreeMap<Integer, SingleReadAlignment>(); //TODO Move this to ContigSequenceDataProvider
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private boolean dirty = false;
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public AlignmentEditor()
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{
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super();
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conversationHolder = CdmStore.createConversation();
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//conversationHolder = null;
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}
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private void refreshToolbarElement(String id) {
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ICommandService commandService =
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(ICommandService)PlatformUI.getWorkbench().getActiveWorkbenchWindow().getService(ICommandService.class);
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if (commandService != null) {
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commandService.refreshElements(id, Collections.EMPTY_MAP);
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}
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}
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private void registerEditSettingListener(MultipleAlignmentsContainer container) {
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container.getEditSettings().addListener(new EditSettingsListener() {
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@Override
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public void workingModeChanged(EditSettingsChangeEvent e) {} // Currently nothing to do
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@Override
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public void insertLeftInDataAreaChanged(EditSettingsChangeEvent e) {
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updateStatusBar();
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refreshToolbarElement(ToggleLeftRightInsertionHandler.COMMAND_ID);
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}
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@Override
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public void insertChanged(EditSettingsChangeEvent e) {
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updateStatusBar();
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refreshToolbarElement(ToggleInsertOverwriteHandler.COMMAND_ID);
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}
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});
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}
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private AlignmentArea createIndexArea(MultipleAlignmentsContainer container, AlignmentArea labeledArea) {
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AlignmentArea result = new AlignmentArea(container);
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result.setAllowVerticalScrolling(false);
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result.getDataAreas().getTopAreas().add(new SequenceIndexArea(result.getContentArea(), labeledArea));
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return result;
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}
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private AlignmentArea createEditableAlignmentArea(MultipleAlignmentsContainer container, boolean allowVerticalScrolling) {
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AlignmentArea result = new AlignmentArea(container);
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result.setAllowVerticalScrolling(allowVerticalScrolling);
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CharacterTokenSet tokenSet = CharacterTokenSet.newDNAInstance(); //TODO Should NUCLEOTIDE be used instead?
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AlignmentModel<Character> provider = new PackedAlignmentModel<Character>(tokenSet);
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result.setAlignmentModel(provider, false);
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provider.getChangeListeners().add(DIRTY_LISTENER);
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result.getPaintSettings().getTokenPainterList().set(0, new NucleotideTokenPainter());
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return result;
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}
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private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container,
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AlignmentArea labeledArea) {
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AlignmentArea result = new AlignmentArea(container);
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result.setAllowVerticalScrolling(false);
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result.getDataAreas().getBottomAreas().add(
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new ConsensusSequenceArea(result.getContentArea(), labeledArea));
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return result;
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}
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private MultipleAlignmentsContainer getAlignmentsContainer() {
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if (alignmentsContainer == null) {
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alignmentsContainer = new MultipleAlignmentsContainer();
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AlignmentAreaList list = alignmentsContainer.getAlignmentAreas();
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AlignmentArea readsArea = createEditableAlignmentArea(alignmentsContainer, true);
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readsArea.getSelection().addSelectionListener(ACTION_UPDATER);
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list.add(createIndexArea(alignmentsContainer, readsArea));
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list.add(readsArea); // Make sure READS_AREA_INDEX is correct.
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AlignmentArea editableConsensusArea = createEditableAlignmentArea(alignmentsContainer, false);
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editableConsensusArea.getSelection().addSelectionListener(ACTION_UPDATER);
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list.add(editableConsensusArea); // Make sure COMSENSUS_AREA_INDEX is correct.
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list.add(createConsensusHintArea(alignmentsContainer, readsArea));
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registerEditSettingListener(alignmentsContainer);
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}
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return alignmentsContainer;
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}
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public AlignmentArea getReadsArea() {
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return getAlignmentsContainer().getAlignmentAreas().get(READS_AREA_INDEX);
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}
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public AlignmentArea getEditableConsensusArea() {
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return getAlignmentsContainer().getAlignmentAreas().get(EDITABLE_CONSENSUS_AREA_INDEX);
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}
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/**
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* Checks whether {@link #getReadsArea()} or {@link #getEditableConsensusArea()} currently
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* have the user focus and returns the according component.
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*
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* @return either the reads or the consensus alignment area or {@code null} if none of these
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* components is currently focused
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*/
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public AlignmentArea getFocusedArea() {
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AlignmentArea result = getReadsArea();
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if (hasFocus(result)) {
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return result;
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}
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else {
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result = getEditableConsensusArea();
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if (hasFocus(result)) {
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return result;
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}
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else {
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return null;
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}
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}
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}
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/**
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* Checks whether the specified alignment area or one of its subcomponents currently has the
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* focus.
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*
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* @param area the alignment area to be checked (Can only be {@link #getReadsArea()} or
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* {@link #getEditableConsensusArea()}.)
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* @return {@code true} if the specified component is focused and is either equal to
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* {@link #getReadsArea()} or {@link #getEditableConsensusArea()}or {@code false} otherwise
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*/
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private boolean hasFocus(AlignmentArea area) {
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return SWTUtils.childHasFocus((Composite)area.getToolkitComponent());
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}
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public boolean hasPherogram(int sequenceID) {
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return getReadsArea().getDataAreas().getSequenceAreas(sequenceID).size() > PHEROGRAM_AREA_INDEX;
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}
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public PherogramArea getPherogramArea(int sequenceID) {
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if (hasPherogram(sequenceID)) {
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return (PherogramArea)getReadsArea().getDataAreas().getSequenceAreas(sequenceID).get(PHEROGRAM_AREA_INDEX);
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}
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else {
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return null;
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}
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}
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private ConsensusSequenceArea getConsensusHintDataArea() {
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return (ConsensusSequenceArea)getAlignmentsContainer().getAlignmentAreas().
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get(CONSENSUS_HINT_AREA_INDEX).getDataAreas().getBottomAreas().
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get(CONSENSUS_DATA_AREA_INDEX);
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}
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@Deprecated //TODO Remove as soon as testing period is over
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private void createTestContents() {
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// Just for testing:
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try {
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addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1").toURI(), false);
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//addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1").toURI(), false);
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addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/Test_qualityScore.scf").toURI(), false);
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// Add test consensus sequence:
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AlignmentModel consensusModel = getEditableConsensusArea().getAlignmentModel();
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int id = consensusModel.addSequence(CONSENSUS_NAME);
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Collection<Object> tokens = new ArrayList<Object>(); // First save tokens in a collection to avoid GUI updated for each token.
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tokens.add(consensusModel.getTokenSet().tokenByRepresentation("A"));
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tokens.add(consensusModel.getTokenSet().tokenByRepresentation("C"));
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tokens.add(consensusModel.getTokenSet().tokenByRepresentation("G"));
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tokens.add(consensusModel.getTokenSet().tokenByRepresentation("T"));
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consensusModel.insertTokensAt(id, 0, tokens);
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}
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catch (Exception e) {
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throw new RuntimeException(e);
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}
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}
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private void readCDMData(Sequence sequenceNode) {
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//TODO If called from somewhere else than createPartControl() the editorInput needs to be checked and previous contents need to be cleared (or updated).
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// Add reads:
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for (SingleReadAlignment singleReadAlignment : sequenceNode.getSingleReadAlignments()) {
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try {
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SingleRead pherogramInfo = singleReadAlignment.getSingleRead();
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URI uri = null;
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if (pherogramInfo.getPherogram() != null) {
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uri = MediaUtils.getFirstMediaRepresentationPart(pherogramInfo.getPherogram()).getUri();
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}
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int id = addRead(DerivateLabelProvider.getDerivateText(pherogramInfo, conversationHolder),
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uri,
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singleReadAlignment.isReverseComplement(),
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singleReadAlignment.getEditedSequence(),
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singleReadAlignment.getFirstSeqPosition(),
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singleReadAlignment.getLeftCutPosition(),
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singleReadAlignment.getRightCutPosition(),
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singleReadAlignment.getShifts());
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cdmMap.put(id, singleReadAlignment);
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}
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catch (Exception e) { // Usually due to an error while trying to read the pherogram (e.g. due to an unsupported format or an invalid URI).
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MessagingUtils.errorDialog("Error", null, "A single read was skipped because of the following error:\n\n" +
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e.getLocalizedMessage(), TaxeditorMolecularPlugin.PLUGIN_ID, e, false);
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}
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}
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// Set consensus sequence:
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AlignmentModel consensusProvider = getEditableConsensusArea().getAlignmentModel();
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int id = consensusProvider.addSequence(CONSENSUS_NAME);
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consensusProvider.insertTokensAt(id, 0, AlignmentModelUtils.charSequenceToTokenList(
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sequenceNode.getConsensusSequence().getString(), consensusProvider.getTokenSet()));
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//TODO Can the consensus sequence also be null? / Should it be created here, if nothing is in the DB?
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}
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@Override
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public void createPartControl(Composite parent) {
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SWTComponentFactory.getInstance().getSWTComponent(getAlignmentsContainer(), parent, SWT.NONE);
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Display.getCurrent().addFilter(SWT.FocusIn, ACTION_UPDATER);
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Display.getCurrent().addFilter(SWT.FocusOut, ACTION_UPDATER);
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updateStatusBar();
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if (getEditorInput() instanceof AlignmentEditorInput) {
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if (((AlignmentEditorInput)getEditorInput()).getSequenceNodeUuid() != null) {
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Sequence sequenceNode = CdmStore.getService(ISequenceService.class).load(((AlignmentEditorInput)getEditorInput()).getSequenceNodeUuid());
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//re-load into the current session if it is already persisted in the DB
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if(sequenceNode!=null && sequenceNode.getId()!=0){
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sequenceNode = CdmStore.getService(ISequenceService.class).load(sequenceNode.getUuid());
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}
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readCDMData(sequenceNode);
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}
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else {
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createTestContents(); // This case will removed after the test phase and an exception should probably be thrown.
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}
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}
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else {
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throw new IllegalArgumentException("The editor input must have the type " +
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AlignmentEditorInput.class.getCanonicalName()); //TODO What should be done here?
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}
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}
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@Override
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public void dispose() {
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389
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Display.getCurrent().removeFilter(SWT.FocusIn, ACTION_UPDATER);
|
390
|
Display.getCurrent().removeFilter(SWT.FocusOut, ACTION_UPDATER);
|
391
|
CLIPBOARD.dispose();
|
392
|
super.dispose();
|
393
|
}
|
394
|
|
395
|
|
396
|
private void updateStatusBar() {
|
397
|
IActionBars bars = getEditorSite().getActionBars();
|
398
|
bars.getStatusLineManager().setMessage("Edit mode: " +
|
399
|
(getReadsArea().getEditSettings().isInsert() ? "Insert" : "Overwrite") + " " +
|
400
|
"Insertion in pherogram: " +
|
401
|
(getReadsArea().getEditSettings().isInsertLeftInDataArea() ? "Left" : "Right"));
|
402
|
}
|
403
|
|
404
|
|
405
|
private SingleReadAlignment.Shift[] convertToCDMShifts(PherogramAreaModel model) {
|
406
|
Iterator<ShiftChange> iterator = model.shiftChangeIterator();
|
407
|
List<Shift> shifts = new ArrayList<SingleReadAlignment.Shift>();
|
408
|
while (iterator.hasNext()) {
|
409
|
ShiftChange shiftChange = iterator.next();
|
410
|
shifts.add(new SingleReadAlignment.Shift(shiftChange.getBaseCallIndex(), shiftChange.getShiftChange()));
|
411
|
}
|
412
|
return shifts.toArray(new Shift[]{});
|
413
|
}
|
414
|
|
415
|
|
416
|
@Override
|
417
|
public void doSave(IProgressMonitor monitor) {
|
418
|
if (getEditorInput() instanceof AlignmentEditorInput) {
|
419
|
String taskName = "Saving alignment";
|
420
|
monitor.beginTask(taskName, 3);
|
421
|
|
422
|
//re-loading sequence to avoid session conflicts
|
423
|
Sequence sequenceNode = CdmStore.getService(ISequenceService.class).load(((AlignmentEditorInput)getEditorInput()).getSequenceNodeUuid());
|
424
|
StringAdapter stringProvider = new StringAdapter(getEditableConsensusArea().getAlignmentModel(), false); // Throws an exception if a token has more than one character.
|
425
|
|
426
|
// Write consensus sequence:
|
427
|
SequenceString consensusSequenceObj = sequenceNode.getConsensusSequence();
|
428
|
String newConsensusSequence = stringProvider.getSequence(
|
429
|
getEditableConsensusArea().getAlignmentModel().sequenceIDByName(CONSENSUS_NAME));
|
430
|
if (consensusSequenceObj == null) {
|
431
|
sequenceNode.setConsensusSequence(SequenceString.NewInstance(newConsensusSequence));
|
432
|
}
|
433
|
else {
|
434
|
consensusSequenceObj.setString(newConsensusSequence);
|
435
|
}
|
436
|
|
437
|
// Write single reads:
|
438
|
stringProvider.setUnderlyingProvider(getReadsArea().getAlignmentModel());
|
439
|
sequenceNode.getSingleReadAlignments().retainAll(cdmMap.values()); // Remove all reads that are not in the alignment anymore.
|
440
|
Iterator<Integer> iterator = getReadsArea().getAlignmentModel().sequenceIDIterator();
|
441
|
while (iterator.hasNext()) {
|
442
|
int id = iterator.next();
|
443
|
SingleReadAlignment singleRead = cdmMap.get(id);
|
444
|
if (singleRead == null) {
|
445
|
throw new InternalError("Creating new reads from AlignmentEditor not implemented.");
|
446
|
//TODO Create new read object. => Shall it be allowed to add reads in the alignment editor which are not represented in the CDM tree before the alignment editor is saved?
|
447
|
//singleRead = SingleReadAlignment.NewInstance(consensusSequence, singleRead, shifts, editedSequence);
|
448
|
}
|
449
|
|
450
|
singleRead.setEditedSequence(stringProvider.getSequence(id));
|
451
|
|
452
|
PherogramArea pherogramArea = getPherogramArea(id);
|
453
|
if (pherogramArea != null) {
|
454
|
PherogramAreaModel model = pherogramArea.getModel();
|
455
|
singleRead.setReverseComplement(model.getPherogramProvider() instanceof ReverseComplementPherogramProvider); // Works only if ReverseComplementPherogramProvider instances are not nested.
|
456
|
singleRead.setShifts(convertToCDMShifts(getPherogramArea(id).getModel()));
|
457
|
singleRead.setFirstSeqPosition(model.getFirstSeqPos());
|
458
|
singleRead.setLeftCutPosition(model.getLeftCutPosition());
|
459
|
singleRead.setRightCutPosition(model.getRightCutPosition());
|
460
|
}
|
461
|
}
|
462
|
|
463
|
if (!conversationHolder.isBound()) {
|
464
|
conversationHolder.bind();
|
465
|
}
|
466
|
monitor.worked(1);
|
467
|
|
468
|
// Commit the conversation and start a new transaction immediately:
|
469
|
conversationHolder.commit(true);
|
470
|
monitor.worked(1);
|
471
|
|
472
|
dirty = false;
|
473
|
monitor.worked(1);
|
474
|
monitor.done();
|
475
|
firePropertyChange(PROP_DIRTY);
|
476
|
}
|
477
|
else {
|
478
|
//TODO Throw exception as soon as testing period which allows unlinked AlignmentEditor is over.
|
479
|
}
|
480
|
}
|
481
|
|
482
|
|
483
|
@Override
|
484
|
public void doSaveAs() {}
|
485
|
|
486
|
|
487
|
@Override
|
488
|
public void init(IEditorSite site, IEditorInput input) throws PartInitException {
|
489
|
setSite(site);
|
490
|
setInput(input);
|
491
|
}
|
492
|
|
493
|
|
494
|
@Override
|
495
|
public boolean isDirty() {
|
496
|
return dirty;
|
497
|
}
|
498
|
|
499
|
|
500
|
private void setDirty() {
|
501
|
dirty = true;
|
502
|
firePropertyChange(IEditorPart.PROP_DIRTY);
|
503
|
}
|
504
|
|
505
|
|
506
|
@Override
|
507
|
public boolean isSaveAsAllowed() {
|
508
|
return false; // "Save as" not allowed.
|
509
|
}
|
510
|
|
511
|
|
512
|
@Override
|
513
|
public void setFocus() {
|
514
|
if(conversationHolder != null){
|
515
|
conversationHolder.bind();
|
516
|
}
|
517
|
}
|
518
|
|
519
|
|
520
|
public boolean isInsertMode() {
|
521
|
return getAlignmentsContainer().getEditSettings().isInsert();
|
522
|
}
|
523
|
|
524
|
|
525
|
public boolean isInsertLeftInPherogram() {
|
526
|
return getAlignmentsContainer().getEditSettings().isInsertLeftInDataArea();
|
527
|
}
|
528
|
|
529
|
|
530
|
public void toggleLeftRightInsertionInPherogram() {
|
531
|
getAlignmentsContainer().getEditSettings().toggleInsertLeftInDataArea();
|
532
|
}
|
533
|
|
534
|
|
535
|
public void toggleInsertOverwrite() {
|
536
|
getAlignmentsContainer().getEditSettings().toggleInsert();
|
537
|
}
|
538
|
|
539
|
|
540
|
private String cutPherogram(boolean left) {
|
541
|
SelectionModel selection = getReadsArea().getSelection();
|
542
|
if (selection.getCursorHeight() != 1) {
|
543
|
return "Cutting pherograms is only possible if exactly one row is selected.";
|
544
|
}
|
545
|
else {
|
546
|
PherogramArea pherogramArea =
|
547
|
getPherogramArea(getReadsArea().getSequenceOrder().idByIndex(selection.getCursorRow()));
|
548
|
if (pherogramArea == null) {
|
549
|
return "There is no pherogram attached to the current sequence.";
|
550
|
}
|
551
|
else {
|
552
|
if (left) {
|
553
|
if (pherogramArea.setLeftCutPositionBySelection()) {
|
554
|
return null;
|
555
|
}
|
556
|
else {
|
557
|
return "The left end of the selection lies outside the pherogram attached to this sequence.";
|
558
|
}
|
559
|
}
|
560
|
else {
|
561
|
if (pherogramArea.setRightCutPositionBySelection()) {
|
562
|
return null;
|
563
|
}
|
564
|
else {
|
565
|
return "The right end of the selection lies outside the pherogram attached to this sequence.";
|
566
|
}
|
567
|
}
|
568
|
}
|
569
|
}
|
570
|
}
|
571
|
|
572
|
|
573
|
public String cutPherogramLeft() {
|
574
|
return cutPherogram(true);
|
575
|
}
|
576
|
|
577
|
|
578
|
public String cutPherogramRight() {
|
579
|
return cutPherogram(false);
|
580
|
}
|
581
|
|
582
|
|
583
|
public void reverseComplementSelectedSequences() {
|
584
|
SelectionModel selection = getReadsArea().getSelection();
|
585
|
AlignmentModel<?> model = getReadsArea().getAlignmentModel();
|
586
|
for (int row = selection.getFirstRow(); row < selection.getFirstRow() + selection.getCursorHeight(); row++) {
|
587
|
int sequenceID = getReadsArea().getSequenceOrder().idByIndex(row);
|
588
|
PherogramArea area = getPherogramArea(sequenceID);
|
589
|
PherogramAreaModel pherogramAlignmentModel = area.getModel();
|
590
|
AlignmentModelUtils.reverseComplement(model, sequenceID,
|
591
|
pherogramAlignmentModel.editableIndexByBaseCallIndex(
|
592
|
pherogramAlignmentModel.getLeftCutPosition()).getBeforeValidIndex(),
|
593
|
pherogramAlignmentModel.editableIndexByBaseCallIndex(
|
594
|
pherogramAlignmentModel.getRightCutPosition()).getAfterValidIndex());
|
595
|
pherogramAlignmentModel.reverseComplement();
|
596
|
}
|
597
|
}
|
598
|
|
599
|
|
600
|
/**
|
601
|
* Recreates the whole consensus sequence from all single read sequences. The previous consensus
|
602
|
* sequence is overwritte.
|
603
|
*/
|
604
|
@SuppressWarnings("unchecked")
|
605
|
public <T> void createConsensusSequence() {
|
606
|
ConsensusSequenceArea area = getConsensusHintDataArea();
|
607
|
AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel();
|
608
|
int sequenceID = model.sequenceIDIterator().next(); // There is always one sequence contained.
|
609
|
int length = getReadsArea().getAlignmentModel().getMaxSequenceLength();
|
610
|
|
611
|
Collection<T> tokens = new ArrayList<T>(length);
|
612
|
for (int column = 0; column < length; column++) {
|
613
|
tokens.add(model.getTokenSet().tokenByRepresentation(area.getConsensusToken(column)));
|
614
|
}
|
615
|
|
616
|
model.removeTokensAt(sequenceID, 0, model.getSequenceLength(sequenceID));
|
617
|
model.insertTokensAt(sequenceID, 0, tokens);
|
618
|
}
|
619
|
|
620
|
|
621
|
/**
|
622
|
* Updates the current consensus sequence by replacing gaps by the according consensus tokens
|
623
|
* calculated from the single read sequences and extends the consensus sequence if necessary.
|
624
|
*/
|
625
|
@SuppressWarnings("unchecked")
|
626
|
public <T> void updateConsensusSequence() {
|
627
|
ConsensusSequenceArea area = getConsensusHintDataArea();
|
628
|
AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel();
|
629
|
TokenSet<T> tokenSet = model.getTokenSet();
|
630
|
int sequenceID = model.sequenceIDIterator().next(); // There is always one sequence contained.
|
631
|
int currentConsensusLength = model.getSequenceLength(sequenceID);
|
632
|
int overallLength = getReadsArea().getAlignmentModel().getMaxSequenceLength();
|
633
|
|
634
|
// Replace gaps by new information:
|
635
|
for (int column = 0; column < currentConsensusLength; column++) {
|
636
|
if (tokenSet.isGapToken(model.getTokenAt(sequenceID, column))) {
|
637
|
T newToken = tokenSet.tokenByRepresentation(area.getConsensusToken(column));
|
638
|
if (!tokenSet.isGapToken(newToken)) {
|
639
|
model.setTokenAt(sequenceID, column, newToken);
|
640
|
}
|
641
|
}
|
642
|
}
|
643
|
|
644
|
// Append additional tokens:
|
645
|
if (overallLength > currentConsensusLength) {
|
646
|
Collection<T> tokens = new ArrayList<T>(overallLength);
|
647
|
for (int column = currentConsensusLength; column < overallLength; column++) {
|
648
|
tokens.add(tokenSet.tokenByRepresentation(area.getConsensusToken(column)));
|
649
|
}
|
650
|
model.appendTokens(sequenceID, tokens);
|
651
|
}
|
652
|
}
|
653
|
|
654
|
|
655
|
public static PherogramProvider readPherogram(URI uri) throws IOException, UnsupportedChromatogramFormatException {
|
656
|
PherogramProvider result;
|
657
|
InputStream stream = uri.toURL().openStream();
|
658
|
try {
|
659
|
result = new BioJavaPherogramProvider(ChromatogramFactory.create(stream));
|
660
|
}
|
661
|
finally {
|
662
|
stream.close();
|
663
|
}
|
664
|
return result;
|
665
|
}
|
666
|
|
667
|
|
668
|
private String newReadName() {
|
669
|
int index = 1;
|
670
|
while (getReadsArea().getAlignmentModel().sequenceIDByName(DEFAULT_READ_NAME_PREFIX + index)
|
671
|
!= AlignmentModel.NO_SEQUENCE_FOUND) {
|
672
|
|
673
|
index++;
|
674
|
}
|
675
|
return DEFAULT_READ_NAME_PREFIX + index;
|
676
|
}
|
677
|
|
678
|
|
679
|
public void addRead(URI pherogramURI, boolean reverseComplemented) throws IOException, UnsupportedChromatogramFormatException {
|
680
|
addRead(newReadName(), pherogramURI, reverseComplemented, null, null, null, null, null);
|
681
|
}
|
682
|
|
683
|
|
684
|
/**
|
685
|
* Adds a new sequence with attached phergram data area to the reads alignment.
|
686
|
* <p>
|
687
|
* If {@code null} is specified as {@code editedSequence} the base call sequence from the pherogram will
|
688
|
* be set as the edited sequence. If {@code null} is specified as {@code shifts} no shifts between the edited
|
689
|
* and the base calls sequence are assumed.
|
690
|
*
|
691
|
* @param name the name of the new sequence
|
692
|
* @param pherogramURI the URI where the associated pherogram file is located
|
693
|
* @param reverseComplemented Specify {@code true} here, if the reverse complement of the pherogram data should
|
694
|
* be added, {@code false} otherwise.
|
695
|
* @param editedSequence the edited version of the base call sequence (May be {@code null}.)
|
696
|
* @param shifts the alignment information that links the edited and the base call sequence (May be {@code null}.)
|
697
|
* @return the sequence ID of the added read
|
698
|
* @throws IOException if an error occurred when trying to read the pherogram file
|
699
|
* @throws UnsupportedChromatogramFormatException if the format of the pherogram file is not supported
|
700
|
*/
|
701
|
public int addRead(String name, URI pherogramURI, boolean reverseComplemented, String editedSequence,
|
702
|
Integer firstSeqPos, Integer leftCutPos, Integer rightCutPos, SingleReadAlignment.Shift[] shifts)
|
703
|
throws IOException, UnsupportedChromatogramFormatException {
|
704
|
|
705
|
AlignmentModel provider = getReadsArea().getAlignmentModel();
|
706
|
PherogramProvider pherogramProvider = null;
|
707
|
if (pherogramURI != null) {
|
708
|
pherogramProvider = readPherogram(pherogramURI); // Must happen before a sequence is added, because it might throw an exception.
|
709
|
if (reverseComplemented) {
|
710
|
pherogramProvider = new ReverseComplementPherogramProvider(pherogramProvider);
|
711
|
}
|
712
|
}
|
713
|
|
714
|
// Create sequence:
|
715
|
provider.addSequence(name);
|
716
|
int id = provider.sequenceIDByName(name);
|
717
|
|
718
|
// Set edited sequence:
|
719
|
Collection<Object> tokens = null; // First save tokens in a collection to avoid GUI updated for each token.
|
720
|
if (editedSequence != null) {
|
721
|
tokens = AlignmentModelUtils.charSequenceToTokenList(editedSequence, provider.getTokenSet());
|
722
|
}
|
723
|
else if (pherogramProvider != null) { // Copy base call sequence into alignment:
|
724
|
tokens = new ArrayList<Object>();
|
725
|
for (int i = 0; i < pherogramProvider.getSequenceLength(); i++) {
|
726
|
tokens.add(provider.getTokenSet().tokenByRepresentation(
|
727
|
Character.toString(pherogramProvider.getBaseCall(i))));
|
728
|
}
|
729
|
setDirty();
|
730
|
}
|
731
|
|
732
|
if (tokens != null) { // If either an edited sequence or a pherogram URI was provided.
|
733
|
provider.insertTokensAt(id, 0, tokens);
|
734
|
|
735
|
if (pherogramProvider != null) {
|
736
|
// Create pherogram area:
|
737
|
PherogramArea pherogramArea = new PherogramArea(getReadsArea().getContentArea(),
|
738
|
new PherogramAreaModel(pherogramProvider));
|
739
|
|
740
|
// Set position properties and shifts:
|
741
|
PherogramAreaModel model = pherogramArea.getModel();
|
742
|
if ((firstSeqPos != null) && (leftCutPos != null)) {
|
743
|
model.setFirstSeqLeftCutPos(firstSeqPos, leftCutPos);
|
744
|
}
|
745
|
if (rightCutPos != null) {
|
746
|
model.setRightCutPosition(rightCutPos);
|
747
|
}
|
748
|
if ((shifts != null) && (shifts.length > 0)) {
|
749
|
for (int i = 0; i < shifts.length; i++) {
|
750
|
model.addShiftChange(shifts[i].position, shifts[i].shift);
|
751
|
}
|
752
|
setDirty();
|
753
|
}
|
754
|
|
755
|
// Add pherogram area to GUI:
|
756
|
pherogramArea.addMouseListener(new PherogramMouseListener(pherogramArea));
|
757
|
getReadsArea().getDataAreas().getSequenceAreas(id).add(pherogramArea);
|
758
|
}
|
759
|
}
|
760
|
return id;
|
761
|
}
|
762
|
}
|